Nextflow workflow report

[stoic_hopper] (resumed run)

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'prepGWAS_shah'

Caused by:
  Process `prepGWAS_shah` terminated with an error exit status (1)

Command executed:

  module load gcc/11.4.0 openmpi/4.1.4 R/4.3.1
  
  # Run analysis script
  Rscript /standard/vol185/cphg_Manichaikul/users/csm6hg/nextflow_dna/scripts/standardize_GWAS_eQTL_for_coloc_new.R \
      --gwas ShahS_31919418_HeartFailure.gz \
      --prefix shah20_gwas_HF \
      --liftover TRUE

Command exit status:
  1

Command output:
  [1] "Finished standardizing columns"
  [1] "Processing LiftOver!"

Command error:
  
  The following object is masked from ‘package:utils’:
  
      findMatches
  
  The following objects are masked from ‘package:base’:
  
      expand.grid, I, unname
  
  Loading required package: IRanges
  
  Attaching package: ‘IRanges’
  
  The following object is masked from ‘package:lubridate’:
  
      %within%
  
  The following objects are masked from ‘package:dplyr’:
  
      collapse, desc, slice
  
  The following object is masked from ‘package:purrr’:
  
      reduce
  
  The following object is masked from ‘package:data.table’:
  
      shift
  
  Loading required package: GenomeInfoDb
  Discarding unchained sequences: 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 5, 6, 7, 8, 9, 1, 2, 3, 4
  Loading required package: BSgenome
  Loading required package: Biostrings
  Loading required package: XVector
  
  Attaching package: ‘XVector’
  
  The following object is masked from ‘package:purrr’:
  
      compact
  
  
  Attaching package: ‘Biostrings’
  
  The following object is masked from ‘package:base’:
  
      strsplit
  
  Error: object 'gwasTest' not found
  Execution halted

Work dir:
  /sfs/ceph/standard/vol185/cphg_Manichaikul/users/csm6hg/nextflow_dna/work/14/54e4fd2773cdbd346aa6036630fa63

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Run times
20-Mar-2025 13:50:11 - 20-Mar-2025 13:53:07 (duration: 2m 56s)
  0 succeeded  
  2426 cached  
  0 ignored  
  3 failed  
Nextflow command
nextflow run main_process.nf -profile slurm -resume -bg
CPU-Hours
3'099.9 (100% cached, 0% failed)
Launch directory
/sfs/ceph/standard/vol185/cphg_Manichaikul/users/csm6hg/nextflow_dna
Work directory
/sfs/ceph/standard/vol185/cphg_Manichaikul/users/csm6hg/nextflow_dna/work
Project directory
/sfs/ceph/standard/vol185/cphg_Manichaikul/users/csm6hg/nextflow_dna
Script name
main_process.nf
Script ID
ec6934758e438790c048328bdca43b36
Workflow session
a324e47c-2917-4670-abd9-b331a64efb5b
Workflow profile
slurm
Nextflow version
version 23.04.1, build 5867 (15-04-2023 07:31 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)